* Identify the potential historical interactions that might have lead to the development of genomic adaptations.

* Identify the potential historical interactions that might have lead to the development of genomic adaptations.

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Through a case study on ''Plasmodium'' evolution, we will illustrate how CoGe can be used for the analysis of multigene families, local synteny, and whole genome comparisons (genome composition, rearrangement events, and gene order conservation).

== '''Finding and integrating Plasmodium genomes in CoGe ''' ==

== '''Finding and integrating Plasmodium genomes in CoGe ''' ==

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You can find the details of Plasmodium genome integration in the following link: [[Finding and intregating Plasmodium genomes to CoGe]]

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You can find the details of ''Plasmodium'' spp. genome integration in the following link: [[Finding and intregating Plasmodium genomes to CoGe]]

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=='''Using CoGe tools to perform comparative analyses'''==

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=='''Comparative analyses workflows'''==

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==='''Workflows'''===

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The following links direct to specific tools for the comparative analysis of ''Plasmodium'' genomes:

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The following links direct to specific tools for the comparative analysis of Plasmodium genomes:

You can learn about the SPA usage on ''Plasmodium genomes'' in the following link: [[Plasmodium genome analysis using Syntenic Path Assembly]]

=='''Overall conclusions'''==

=='''Overall conclusions'''==

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The number of available ''Plasmodium'' genomes has increased considerably during recent years. This wealth of genomic information creates an unprecedented opportunity to study the unique genomic qualities of this genus using comparative genomics.

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Insights into the unique patterns of ''Plasmodium'' biology, epidemiology, ecology, and genetics can be obtained from molecular and comparative genomic studies. The rapid growth of genomic information makes implementing tools that facilitate assessing genome evolutionary trends an imperative task. The services and tools provided by the CoGe platform are of considerable use in advancing ''Plasmodium'' comparative genomics. Here, we showed how various CoGe tools could be used to assess evolutionary patterns unique to ''Plasmodium''. We also showed how to use this platform to further characterize sequenced ''Plasmodium'' genomes. Overall, we have demonstrated that CoGe’s tools can be used to address evolutionary questions such as:

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There have been tremendous achievements in malaria treatment and control strategies. Thanks to worldwide efforts, there has been a significant reduction in the number of malaria cases and malaria-related deaths between 2000 and 2015. By 2015, it was estimated that the number of malaria cases decreased from 262 million to 214 million, and the number of malaria-related deaths from 839,000 to 438,000 <ref>World Health Organization. (2015). World Malaria Report 2015. Retrieved from http://www.who.int/malaria/publications/world-malaria-report-2015/report/en/</ref>. However, there are still numerous aspects of malaria research that need to be further addressed.

The rapid growth of genomic information makes implementing tools that facilitate assessing genome evolutionary trends an imperative task. The services and tools provided by the CoGe platform are of considerable use in advancing ''Plasmodium'' comparative genomics. Here, we showed how various CoGe tools could be used to assess evolutionary patterns unique to ''Plasmodium''. We also showed how to use this platform to further characterize sequenced ''Plasmodium'' genomes. Overall, we have demonstrated that CoGe’s tools can be used to address evolutionary questions such as:

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*The evolutionary origins of ''Laveranian'' AT-rich genomes.

*The evolutionary origins of ''Laveranian'' AT-rich genomes.

*The location and nature of genome rearrangements between ''Plasmodium''.

*The location and nature of genome rearrangements between ''Plasmodium''.

About this guide

This 'cookbook' style document is meant to provide an introduction to many of our tools and services and is structured around a case study of investigating genome evolution of the malaria-causing Plasmodium spp. The small size and unique features of this pathogen's genome make it ideal for beginning to understand how our tools can be used to conduct comparative genomic analyses and uncover meaningful discoveries.

Through a number of example analyses, this guide will teach users about the following tools:

A brief introduction to Plasmodium genome evolution

The genus Plasmodium emerged ~40 million years ago and harbors roughly 200 species of parasitic protozoa better known as malaria parasites. All Plasmodium species have a complex life cycle involving some kind of vertebrate host and a mosquito vector. In addition, Plasmodium species share similar life cycle characteristics, albeit with a few exceptions (e.g. hypnozoites). Plasmodium genomes are tiny (between 17-28Mb) in comparison to those of their vertebrate (1Gb for birds; 2-3Gb for mammals) and mosquito (230–284Mbp) hosts [1]. All Plasmodium genomes consist of fourteen chromosomes (nuclear genome), as well as a mitochondrial and apicoplast genome. Despite these shared genomic characteristics, the structural organization, gene content, and sequence of Plasmodium genomes is highly variably within the genus [2]. The exact origins and mechanisms of these differences remain largely unexplored, however, they are generally hypothesized to stem from host shift events [3][4].

An increase in funding devoted to malaria research has coincided with a dramatic increase in publicly available genomic information for Plasmodium[5]. The most prominent repository is found at NCBI/Genbank [6]; while additional and unique sequences can also be found on other databases: PlasmoDB[7], GeneDB[8], and MalAvi[9]. This wealth of genomic data facilitates detailed comparative genomic approaches, opening the possibility to:

Overall conclusions

Insights into the unique patterns of Plasmodium biology, epidemiology, ecology, and genetics can be obtained from molecular and comparative genomic studies. The rapid growth of genomic information makes implementing tools that facilitate assessing genome evolutionary trends an imperative task. The services and tools provided by the CoGe platform are of considerable use in advancing Plasmodium comparative genomics. Here, we showed how various CoGe tools could be used to assess evolutionary patterns unique to Plasmodium. We also showed how to use this platform to further characterize sequenced Plasmodium genomes. Overall, we have demonstrated that CoGe’s tools can be used to address evolutionary questions such as: